Is there any way to automatically deploy to a server after I build a flex app, and then debug using the remote url ?
This is totally possible in FlashBuilder, but I am
You can script any action you want in a batch file and then go to Project->Properties->Build->Post-build-command and enter your batch file execution line.
To jump to a debug URL after compiling, just go into Project->Properties->Output, select "Open document" and type your URL.
If you deploy a debug version of your SWF, you can start FlashDevelop debugger for remote debugging (see Debug menu) and then navigate to the online page where your SWF resides.